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ORCIDBMC Bioinformatics, Volume 18
Volume 18, Number 1, December 2017
- Dongmei Li
, Zidian Xie, Martin S. Zand, Thomas Fogg, Timothy D. Dye:
Bon-EV: an improved multiple testing procedure for controlling false discovery rates. 1:1-1:10 - Annika Röhl, Alexander Bockmayr:
A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks. 2:1-2:10 - Johannes W. R. Martini, Ning Gao, Diercles F. Cardoso, Valentin Wimmer, Malena Erbe, Rodolfo J. C. Cantet, Henner Simianer:
Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE). 3:1-3:16 - Xinyan Zhang, Himel Mallick, Zaixiang Tang, Lei Zhang, Xiangqin Cui, Andrew K. Benson, Nengjun Yi:
Negative binomial mixed models for analyzing microbiome count data. 4:1-4:10 - Davoud Torkamaneh, Jérôme Laroche, Maxime Bastien, Amina Abed, François Belzile:
Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data. 5:1-5:7 - Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, Emanuel Weitschek:
TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas. 6:1-6:9 - Michael Piechotta, Emanuel Wyler, Uwe Ohler, Markus Landthaler, Christoph Dieterich:
JACUSA: site-specific identification of RNA editing events from replicate sequencing data. 7:1-7:15 - Ariane L. Hofmann, Jonas Behr, Jochen Singer, Jack Kuipers, Christian Beisel, Peter Schraml, Holger Moch, Niko Beerenwinkel:
Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. 8:1-8:15 - Milos D. Radovic, Mohamed F. Ghalwash, Nenad Filipovic, Zoran Obradovic:
Minimum redundancy maximum relevance feature selection approach for temporal gene expression data. 9:1-9:14 - Shirin Taghipour, Peyman Zarrineh, Mohammad Ganjtabesh, Abbas Nowzari-Dalini:
Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources. 10:1-10:9 - Robin Kobus, Christian Hundt, André Müller, Bertil Schmidt:
Accelerating metagenomic read classification on CUDA-enabled GPUs. 11:1-11:10 - Fabian Grandke, Soumya Ranganathan, Nikkie van Bers, Jorn R. de Haan, Dirk Metzler:
PERGOLA: fast and deterministic linkage mapping of polyploids. 12:1-12:9 - Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos, Grigoris D. Amoutzias:
T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes. 13:1-13:8 - Thomas S. Wingo, Alex Kotlar, David J. Cutler:
MPD: multiplex primer design for next-generation targeted sequencing. 14:1-14:5 - Jinyu Li, Jörg Vervoorts, Paolo Carloni, Giulia Rossetti, Bernhard Lüscher:
Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant. 15:1-15:9 - Sameh Eid, Samo Turk, Andrea Volkamer, Friedrich Rippmann, Simone Fulle:
KinMap: a web-based tool for interactive navigation through human kinome data. 16:1-16:6 - Nicolas Bosc, Christophe Meyer, Pascal Bonnet:
The use of novel selectivity metrics in kinase research. 17:1-17:12 - Wen Zhang, Yanlin Chen, Feng Liu, Fei Luo, Gang Tian, Xiaohong Li:
Predicting potential drug-drug interactions by integrating chemical, biological, phenotypic and network data. 18:1-18:12 - Katrin Tebel, Vivien Boldt, Anne Steininger, Matthias Port, Grit Ebert, Reinhard Ullmann:
GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants. 19:1-19:8 - Hashem A. Shihab, Mark F. Rogers, Michael Ferlaino, Colin Campbell, Tom R. Gaunt:
GTB - an online genome tolerance browser. 20:1-20:6 - Reedik Mägi, Yury V. Suleimanov, Geraldine M. Clarke, Marika Kaakinen, Krista Fischer, Inga Prokopenko, Andrew P. Morris:
SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes. 25:1-25:8 - Roberto A. Barrero, Kathryn R. Napier, James Cunnington, Lia Liefting, Sandi Keenan, Rebekah A. Frampton, Tamás O. Szabó, Simon Bulman, Adam Hunter, Lisa Ward, Mark Whattam, Matthew I. Bellgard:
An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids. 26:1-26:12 - Zhi-Ping Liu, Shutang Liu, Ruitang Chen, Xiaopeng Huang, Ling-Yun Wu:
Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces. 27:1-27:13 - Seyed Amir Malekpour, Hamid Pezeshk, Mehdi Sadeghi:
PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities. 30:1-30:11 - Wei-Sheng Wu, Meng-Jhun Jhou:
MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm. 31:1-31:10 - Nikhil Cheerla, Olivier Gevaert:
MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation. 32:1-32:11 - Marco Albrecht, Damian Stichel, Benedikt Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn, Franziska Matthäus:
TTCA: an R package for the identification of differentially expressed genes in time course microarray data. 33:1-33:11 - Sylvester Olubolu Orimaye, Jojo Sze-Meng Wong, Karen Jennifer Golden, Chee Piau Wong, Ireneous N. Soyiri:
Predicting probable Alzheimer's disease using linguistic deficits and biomarkers. 34:1-34:13 - Yi-Pin Lai, Liang-Bo Wang, Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang:
iGC - an integrated analysis package of gene expression and copy number alteration. 35:1-35:9 - Carles Hernandez-Ferrer, Carlos Ruiz-Arenas, Alba Beltran-Gomila, Juan R. González:
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. 36:1-36:7 - Rashmi R. Hazarika, Barbara De Coninck, Lidia R. Yamamoto, Laura R. Martin, Bruno P. A. Cammue, Vera van Noort:
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. 37:1-37:9 - Claire R. Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim:
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq. 38:1-38:12 - Yiding Lu, Yufan Guo, Anna Korhonen:
Link prediction in drug-target interactions network using similarity indices. 39:1-39:9 - Noah Eyal-Altman, Mark Last, Eitan Rubin:
PCM-SABRE: a platform for benchmarking and comparing outcome prediction methods in precision cancer medicine. 40:1-40:7 - N. Ari Wijetunga, Andrew D. Johnston, Ryo Maekawa, Fabien Delahaye, Netha Ulahannan, Kami Kim, John M. Greally:
SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. 41:1-41:13 - Fan Zhang, Patrick Flaherty:
Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data. 45:1-45:10 - Tsukasa Fukunaga, Wataru Iwasaki:
Inactivity periods and postural change speed can explain atypical postural change patterns of Caenorhabditis elegans mutants. 46:1-46:9 - Jiaoyun Yang, Haipeng Wang, Huitong Ding, Ning An, Gil Alterovitz:
Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization. 47:1-47:10 - Hatem Elshazly, Yassine Souilmi, Peter J. Tonellato, Dennis P. Wall, Mohamed Abouelhoda:
MC-GenomeKey: a multicloud system for the detection and annotation of genomic variants. 49:1-49:14 - Ying Li, Xiaohu Shi, Yanchun Liang, Juan Xie, Yu Zhang, Qin Ma:
RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation. 51:1-51:11 - David R. Penas, Patricia González, Jose A. Egea, Ramón Doallo, Julio R. Banga:
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy. 52:1-52:24 - Virginie Stanislas, Cyril Dalmasso, Christophe Ambroise:
Eigen-Epistasis for detecting gene-gene interactions. 54:1-54:14 - Victor Alexandre Padilha, Ricardo J. G. B. Campello:
A systematic comparative evaluation of biclustering techniques. 55:1-55:25 - Michal Jablonski, Jana Starcuková, Zenon Starcuk Jr.:
Processing tracking in jMRUI software for magnetic resonance spectra quantitation reproducibility assurance. 56:1-56:11 - Onur Erbilgin, Benjamin P. Bowen, Suzanne M. Kosina, Stefan Jenkins, Rebecca K. Lau, Trent R. Northen:
Dynamic substrate preferences predict metabolic properties of a simple microbial consortium. 57:1-57:12 - Giulia Paciello, Elisa Ficarra:
FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples. 58:1-58:12 - Yasir Rahmatallah, Boris L. Zybailov, Frank Emmert-Streib, Galina V. Glazko:
GSAR: Bioconductor package for Gene Set analysis in R. 61:1-61:12 - Fereshteh Chitsazian, Mehdi Sadeghi, Elahe Elahi:
Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines. 67:1-67:14 - Rob Eisinga, Tom Heskes, Ben Pelzer, Manfred te Grotenhuis:
Exact p-values for pairwise comparison of Friedman rank sums, with application to comparing classifiers. 68:1-68:18 - Xiaoke Ma, Zaiyi Liu, Zhongyuan Zhang, Xiao-Tai Huang, Wanxin Tang:
Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data. 72:1-72:13 - Orsolya Pipek, Dezso Ribli, János Molnár, Ádam Póti, Marcin Krzystanek, András Bodor, Gábor E. Tusnády, Zoltan Szallasi, István Csabai, David Szüts:
Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut. 73:1-73:11 - Shupeng Gui, Andrew P. Rice, Rui Chen, Liang Wu, Ji Liu, Hongyu Miao:
A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data. 74:1-74:13 - Wutao Lin, Donghong Ji, Yanan Lu:
Disorder recognition in clinical texts using multi-label structured SVM. 75:1-75:11 - Zohar Zafrir, Tamir Tuller:
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. 77:1-77:10 - Govind Nair, Christian Jungreuthmayer, Jürgen Zanghellini:
Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization. 78:1-78:9 - Sinjini Sikdar, Susmita Datta:
A novel statistical approach for identification of the master regulator transcription factor. 79:1-79:11 - Cristiano Lacerda Nunes Pinto, Cristiane Neri Nobre, Luis Enrique Zárate:
Transductive learning as an alternative to translation initiation site identification. 81:1-81:15 - Rui Henriques, Francisco L. Ferreira, Sara C. Madeira:
BicPAMS: software for biological data analysis with pattern-based biclustering. 82:1-82:16 - Mari van Reenen, Johan A. Westerhuis, Carolus J. Reinecke, J. Hendrik Venter:
Metabolomics variable selection and classification in the presence of observations below the detection limit using an extension of ERp. 83:1-83:13 - Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain, Michael Nodzenski, Robert D. Stevens, Olga Ilkayeva, Boyd E. Metzger, Christopher B. Newgard, William L. Lowe Jr., Denise M. Scholtens:
Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data. 84:1-84:17 - James C. Wilgenbusch, Wen Huang, Kyle A. Gallivan:
Visualizing phylogenetic tree landscapes. 85:1-85:12 - Daniel Ian McSkimming, Khaled Rasheed, Natarajan Kannan:
Classifying kinase conformations using a machine learning approach. 86:1-86:15 - Jiapeng Zhou, Jing Xin, Yayun Niu, Shiwen Wu:
DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD. 87:1-87:10 - Vitaly A. Selivanov, Adrián Benito, Anibal Miranda, Esther Aguilar, Ibrahim Halil Polat, Josep J. Centelles, Anusha Jayaraman, Paul W.-N. Lee, Silvia Marin, Marta Cascante:
MIDcor, an R-program for deciphering mass interferences in mass spectra of metabolites enriched in stable isotopes. 88:1-88:9 - Weiwei Ouyang, Qiang An, Jinying Zhao, Huaizhen Qin:
Erratum to: Integrating mean and variance heterogeneities to identify differentially expressed genes. 89:1 - Yanhui Fan, You-Qiang Song:
PyHLA: tests for the association between HLA alleles and diseases. 90:1-90:5 - Seung Hoan Choi, Adam Labadorf, Richard H. Myers, Kathryn L. Lunetta, Josée Dupuis, Anita L. DeStefano:
Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis. 91:1-91:13 - Quan Zhang, Yuzhen Ye:
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. 92:1-92:12 - Hirokazu Chiba, Ikuo Uchiyama:
SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases. 93:1-93:6 - W. Duncan Wadsworth, Raffaele Argiento, Michele Guindani, Jessica Galloway-Pena, Samuel A. Shelburne, Marina Vannucci:
An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data. 94:1-94:12 - Georgios A. Dalkas, Marianne Rooman:
SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence. 95:1-95:12 - Beatriz Serrano-Solano, Antonio Díaz Ramos, Jean-Karim Hériché, Juan A. G. Ranea:
How can functional annotations be derived from profiles of phenotypic annotations? 96:1-96:12 - Raja Ali, Mikael Bark, Jorge Miró, Sayyed Muhammad, Joel Sjöstrand, Syed M. Zubair, Raja M. Abbas, Lars Arvestad:
VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces. 97:1-97:8 - Yanhui Hu, Aram Comjean, Norbert Perrimon, Stephanie E. Mohr:
The Drosophila Gene Expression Tool (DGET) for expression analyses. 98:1-98:9 - Yiming Zuo, Yi Cui, Guoqiang Yu, Ruijiang Li, Habtom W. Ressom:
Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO. 99:1-99:14 - Tran Tuan Anh, Le Thi Ly, Ngo Quoc Viet, Pham The Bao:
Novel methods to optimize gene and statistic test for evaluation - an application for Escherichia coli. 100:1-100:10 - Yanglan Gan, Han Tao, Jihong Guan, Shuigeng Zhou:
iHMS: a database integrating human histone modification data across developmental stages and tissues. 103:1-103:9 - Gabriela F. Rodrigues-Luiz, Mariana S. Cardoso, Hugo O. Valdivia, Edward V. Ayala, Célia M. F. Gontijo, Thiago de S. Rodrigues, Ricardo T. Fujiwara, Robson S. Lopes, Daniella C. Bartholomeu:
TipMT: Identification of PCR-based taxon-specific markers. 104:1-104:8 - Andrew E. Teschendorff, Charles E. Breeze, Shijie C. Zheng, Stephan Beck:
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. 105:1-105:14 - Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan, Amjad Ali:
VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology. 106:1-106:7 - Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W. Ritchie:
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains. 107:1-107:11 - Kosuke Yoshida, Junichiro Yoshimoto, Kenji Doya:
Sparse kernel canonical correlation analysis for discovery of nonlinear interactions in high-dimensional data. 108:1-108:11 - Chunwei Ma, Shaohang Xu, Geng Liu, Xin Liu, Xun Xu, Bo Wen, Siqi Liu:
Improvement of peptide identification with considering the abundance of mRNA and peptide. 109:1-109:8 - Marika Kaakinen, Reedik Mägi, Krista Fischer, Jani Heikkinen, Marjo-Riitta Järvelin, Andrew P. Morris, Inga Prokopenko:
MARV: a tool for genome-wide multi-phenotype analysis of rare variants. 110:1-110:8 - Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S. Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof, Oliver Niehuis:
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. 111:1-111:10 - Francesco Napolitano:
repo: an R package for data-centered management of bioinformatic pipelines. 112:1-112:9 - Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro de Vasconcelos, Fabio Ribeiro Cerqueira:
Erratum to: Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction. 113:1 - Jasmit S. Shah, Shesh N. Rai, Andrew P. DeFilippis, Bradford G. Hill, Aruni Bhatnagar, Guy N. Brock:
Distribution based nearest neighbor imputation for truncated high dimensional data with applications to pre-clinical and clinical metabolomics studies. 114:1-114:13 - Julia Koehler Leman, Sergey Lyskov, Richard Bonneau:
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP. 115:1-115:9 - Matthias Barann, Ralf Zimmer, Fabian Birzele:
Manananggal - a novel viewer for alternative splicing events. 120:1-120:13 - Sergio Gonzalez, Bernardo J. Clavijo, Máximo Rivarola, Patricio Moreno, Paula Fernandez, Joaquín Dopazo, Norma Paniego:
ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. 121:1-121:9 - Lina Yao, Kenneth Wei Min Tan, Tin Wee Tan, Yuan Kun Lee:
Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing. 122:1-122:11 - Diego Pasqualin, Marcos Barbeitos, Fabiano Silva:
SFREEMAP - A simulation-free tool for stochastic mapping. 123:1-123:8 - Massimo Narizzano, Gabriele Arnulfo, Serena Ricci, Benedetta Toselli, Martin Tisdall, Andrea Canessa, Marco Massimo Fato, Francesco Cardinale:
SEEG assistant: a 3DSlicer extension to support epilepsy surgery. 124:1-124:13 - Ilya Zhbannikov, Konstantin G. Arbeev, Igor Akushevich, Eric Stallard, Anatoliy I. Yashin:
stpm: an R package for stochastic process model. 125:1-125:12 - Damoon Nashta-ali, Ali Aliyari, Ahmad Ahmadian Moghadam, Mohammad Amin Edrisi, Abolfazl Seyed Motahari, Babak Hossein Khalaj:
Meta-aligner: long-read alignment based on genome statistics. 126:1-126:9 - Joshua L. Cherry:
A practical exact maximum compatibility algorithm for reconstruction of recent evolutionary history. 127:1-127:12 - Florian Rohart, Aida Eslami, Nicholas Matigian, Stéphanie Bougeard, Kim-Anh Lê Cao:
MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. 128:1-128:13 - Li Zhang, Jason Cham, Alan Paciorek, James Trager, Nadeem Sheikh, Lawrence Fong:
3D: diversity, dynamics, differential testing - a proposed pipeline for analysis of next-generation sequencing T cell repertoire data. 129:1-129:14 - Min Oh, Jaegyoon Ahn, Taekeon Lee, Giup Jang, Chihyun Park, Youngmi Yoon:
Drug voyager: a computational platform for exploring unintended drug action. 131:1-131:13 - Yu-Chiao Chiu, Li-Ju Wang, Tzu-Pin Lu, Tzu-Hung Hsiao, Eric Y. Chuang, Yidong Chen:
Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival. 132:1-132:11 - Sarah Sandmann, Aniek O. de Graaf, Martin Dugas:
BBCAnalyzer: a visual approach to facilitate variant calling. 133:1-133:6 - Xiaoyong Pan, Hong-Bin Shen:
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach. 136:1-136:14 - Saghi Nojoomi, Patrice Koehl:
String kernels for protein sequence comparisons: improved fold recognition. 137:1-137:15 - Philip L. Tzou, Xiaoqiu Huang, Robert W. Shafer:
NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences. 138:1-138:6 - M.-H. Elsensohn, N. Leblay, Sarra Dimassi, Amandine Campan-Fournier, A. Labalme, Florence Roucher Boulez, D. Sanlaville, Gaetan Lesca, C. Bardel, Pascal Roy:
Statistical method to compare massive parallel sequencing pipelines. 139:1-139:11 - Pathima Nusrath Hameed, Karin Verspoor, Snezana Kusljic, Saman K. Halgamuge:
Positive-Unlabeled Learning for inferring drug interactions based on heterogeneous attributes. 140:1-140:15 - Martin Nettling, Hendrik Treutler, Jesús Cerquides, Ivo Grosse:
Combining phylogenetic footprinting with motif models incorporating intra-motif dependencies. 141:1-141:10 - Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar Forner-Martinez, Pablo Marín-García, Vicente Arnau, Peter D'Eustachio, Lincoln Stein, Henning Hermjakob:
Reactome pathway analysis: a high-performance in-memory approach. 142:1-142:9 - Pratyaydipta Rudra, W. Jenny Shi, Brian Vestal, Pamela H. Russell, Aaron Odell, Robin D. Dowell, Richard Radcliffe, Laura M. Saba, Katerina J. Kechris:
Model based heritability scores for high-throughput sequencing data. 143:1-143:16 - Aidi Zhang, Libo He, Yaping Wang:
Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions. 145:1-145:13 - Richard J. Cotton, Birgit Ploier, Michael A. Goren, Anant K. Menon, Johannes Graumann:
flippant-An R package for the automated analysis of fluorescence-based scramblase assays. 146:1-146:7 - Yong Chen, Li Zhao, Yi Wang, Ming Cao, Violet Gelowani, Mingchu Xu, Smriti A. Agrawal, Yumei Li, Stephen P. Daiger, Richard A. Gibbs, Fei Wang, Rui Chen:
SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. 147:1-147:9 - Vera Rieder, Bernhard Blank-Landeshammer, Marleen Stuhr, Tilman Schell, Karsten Biß, Laxmikanth Kollipara, Achim Meyer, Markus Pfenninger, Hildegard Westphal, Albert Sickmann, Jörg Rahnenführer:
DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs. 148:1-148:12 - Hao He, Dongdong Lin, Ji-Gang Zhang, Yu-Ping Wang, Hong-Wen Deng:
Comparison of statistical methods for subnetwork detection in the integration of gene expression and protein interaction network. 149:1-149:6 - Monica H. T. Wong, David M. Mutch, Paul D. McNicholas:
Two-way learning with one-way supervision for gene expression data. 150:1-150:13 - Cedric Simillion, Robin Liechti, Heidi E. L. Lischer, Vassilios Ioannidis, Rémy Bruggmann:
Avoiding the pitfalls of gene set enrichment analysis with SetRank. 151:1-151:14 - Toru Maruyama, Tetsushi Mori, Keisuke Yamagishi, Haruko Takeyama:
SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions. 152:1-152:11 - Paolo Cifani, Mojdeh Shakiba, Sagar Chhangawala, Alex Kentsis:
ProteoModlR for functional proteomic analysis. 153:1-153:7 - Christopher R. Bolen, Florian Rubelt, Jason A. Vander Heiden, Mark M. Davis:
The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires. 155:1-155:8 - Grace Yoon, Yinan Zheng, Zhou Zhang, Haixiang Zhang, Tao Gao, Brian Joyce, Wei Zhang, Weihua Guan, Andrea A. Baccarelli, Wenxin Jiang, Joel Schwartz, Pantel Vokonas, Lifang Hou, Lei Liu:
Ultra-high dimensional variable selection with application to normative aging study: DNA methylation and metabolic syndrome. 156:1-156:7 - Marco Tompitak, Gerard T. Barkema, Helmut Schiessel:
Benchmarking and refining probability-based models for nucleosome-DNA interaction. 157:1-157:7 - Antonio Martín-Navarro, Andrés Gaudioso-Simón, Jorge Álvarez-Jarreta, Julio Montoya, Elvira Mayordomo, Eduardo Ruiz-Pesini:
Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides. 158:1-158:11 - Tim O. F. Conrad, Martin Genzel, Nada Cvetkovic, Niklas Wulkow, Alexander B. Leichtle, Jan Vybíral, Gitta Kutyniok, Christof Schütte:
Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data. 160:1-160:20 - Ricardo Olanda, Mariano Pérez, Juan M. Orduña, Joaquín Tárraga, Joaquín Dopazo:
A new parallel pipeline for DNA methylation analysis of long reads datasets. 161:1-161:6 - Rui Henriques, Francisco L. Ferreira, Sara C. Madeira:
Erratum to: BicPAMS: software for biological data analysis with pattern-based biclustering. 162:1-162:2 - Andrés Becerra, Víctor A. Bucheli, Pedro A. Moreno:
Prediction of virus-host protein-protein interactions mediated by short linear motifs. 163:1-163:11 - Anke Fähnrich, Moritz Krebbel, Normann Decker, Martin Leucker, Felix D. Lange, Kathrin Kalies, Steffen Möller:
ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface. 164:1-164:6 - Tao Huang, Hong Mi, Cheng-Yuan Lin, Ling Zhao, Linda L. D. Zhong, Fengbin Liu, Ge Zhang, Aiping Lu, Zhaoxiang Bian, Shuhai Lin, Man Zhang, Yanhong Li, Dongdong Hu, Chung-Wah Cheng:
MOST: most-similar ligand based approach to target prediction. 165:1-165:11 - Lan Jing, Dandan Guo, Wenjie Hu, Xiaofan Niu:
The prediction of a pathogenesis-related secretome of Puccinia helianthi through high-throughput transcriptome analysis. 166:1-166:13 - Soren H. Hough, Kris Kancleris, Leigh Brody, Neil Humphryes-Kirilov, Joseph Wolanski, Keith Dunaway, Ayokunmi Ajetunmobi, Victor Dillard:
Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments. 167:1-167:10 - Jin Chu Wu, Michael Halter, Raghu N. Kacker, John T. Elliott, Anne L. Plant:
A novel measure and significance testing in data analysis of cell image segmentation. 168:1-168:13 - Li Ma, Suohai Fan:
CURE-SMOTE algorithm and hybrid algorithm for feature selection and parameter optimization based on random forests. 169:1-169:18 - Malik Yousef, Waleed Khalifa, Ilhan Erkin Acar, Jens Allmer:
MicroRNA categorization using sequence motifs and k-mers. 170:1-170:9 - J. Harry Caufield, Christopher Wimble, Shary Semarjit, Stefan Wuchty, Peter Uetz:
Bacterial protein meta-interactomes predict cross-species interactions and protein function. 171:1-171:14 - Kristian Hovde Liland, Hilde Vinje, Lars Snipen:
microclass: an R-package for 16S taxonomy classification. 172:1-172:9 - Daniel Fischer, Mervi Honkatukia, Maria Tuiskula-Haavisto, Klaus Nordhausen, David Cavero, Rudolf Preisinger, Johanna Vilkki:
Subgroup detection in genotype data using invariant coordinate selection. 173:1-173:9 - Alain B. Tchagang, François Fauteux, Dan Tulpan, Youlian Pan:
Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat. 174:1-174:16 - Andrey Smelter, Morgan Astra, Hunter N. B. Moseley:
A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank. 175:1-175:12 - Veit Wiesmann, Matthias Bergler, Ralf Palmisano, Martin Prinzen, Daniela Franz, Thomas Wittenberg:
Using simulated fluorescence cell micrographs for the evaluation of cell image segmentation algorithms. 176:1-176:12 - Qing Wei, Ishita K. Khan, Ziyun Ding, Satwica Yerneni, Daisuke Kihara:
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology. 177:1-177:13 - Emily Jane McTavish, James B. Pettengill, Steve Davis, Hugh Rand, Errol Strain, Marc Allard, Ruth E. Timme:
TreeToReads - a pipeline for simulating raw reads from phylogenies. 178:1-178:7 - Zhi-an Huang, Zhenkun Wen, Qingjin Deng, Ying Chu, Yiwen Sun, Zexuan Zhu:
LW-FQZip 2: a parallelized reference-based compression of FASTQ files. 179:1-179:8 - Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael Vincent, Baohong Zhang:
QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing. 180:1-180:14 - Sk Md Mosaddek Hossain, Sumanta Ray, Anirban Mukhopadhyay:
Preservation affinity in consensus modules among stages of HIV-1 progression. 181:1-181:23 - Willy Vincent Bienvenut, Jean-Pierre Scarpelli, Johan Dumestier, Thierry Meinnel, Carmela Giglione:
EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples. 182:1-182:13 - Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu:
metaX: a flexible and comprehensive software for processing metabolomics data. 183:1-183:14 - Sinan Abo Alchamlat, Frédéric Farnir:
KNN-MDR: a learning approach for improving interactions mapping performances in genome wide association studies. 184:1-184:12 - Erratum to: An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data. 185:1
- Donghyeon Yu, Johan Lim, Xinlei Wang, Faming Liang, Guanghua Xiao:
Enhanced construction of gene regulatory networks using hub gene information. 186:1-186:20 - Giovanna M. M. Ventola, Teresa Maria Rosaria Noviello, Salvatore D'Aniello, Antonietta Spagnuolo, Michele Ceccarelli, Luigi Cerulo:
Identification of long non-coding transcripts with feature selection: a comparative study. 187:1-187:16 - Romain Bourqui, Isabelle Dutour, Jonathan Dubois, William Benchimol, Patricia Thébault:
rNAV 2.0: a visualization tool for bacterial sRNA-mediated regulatory networks mining. 188:1-188:10 - Zhenzhou Wang, Haixing Li:
Generalizing cell segmentation and quantification. 189:1-189:16 - Prabina Kumar Meher, Tanmaya Kumar Sahu, Anjali Banchariya, Atmakuri Ramakrishna Rao:
DIRProt: a computational approach for discriminating insecticide resistant proteins from non-resistant proteins. 190:1-190:14 - Alencar Xavier, Shizhong Xu, William M. Muir, Katy Martin Rainey:
Genomic prediction using subsampling. 191:1-191:7 - Vikram E. Chhatre, Kevin J. Emerson:
StrAuto: automation and parallelization of STRUCTURE analysis. 192:1-192:5 - Hui Peng, Chaowang Lan, Yi Zheng, Gyorgy Hutvagner, Dacheng Tao, Jinyan Li:
Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite. 193:1-193:17 - Beatriz Serrano-Solano, Antonio Díaz Ramos, Jean-Karim Hériché, Juan A. G. Ranea:
Erratum to: How can functional annotations be derived from profiles of phenotypic annotations? 194:1-194:2 - José Santos Reyes, Ángel Monteagudo:
Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability. 195:1-195:18 - Oliver Philipp, Andrea Hamann, Heinz D. Osiewacz, Ina Koch:
The autophagy interaction network of the aging model Podospora anserina. 196:1-196:15 - Zhijiang Wan, Yishan He, Ming Hao, Jian Yang, Ning Zhong:
M-AMST: an automatic 3D neuron tracing method based on mean shift and adapted minimum spanning tree. 197:1-197:13 - Fei Li, Meishan Zhang, Guohong Fu, Donghong Ji:
A neural joint model for entity and relation extraction from biomedical text. 198:1-198:11 - Tobias Madsen, Asger Hobolth, Jens Ledet Jensen, Jakob Skou Pedersen:
Significance evaluation in factor graphs. 199:1-199:12 - Bastijn Koopmans, August B. Smit, Matthijs Verhage, Maarten Loos:
AHCODA-DB: a data repository with web-based mining tools for the analysis of automated high-content mouse phenomics data. 200:1-200:5 - Gaurang Mahajan, Shekhar C. Mande:
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. 201:1-201:14 - Soren H. Hough, Kris Kancleris, Leigh Brody, Neil Humphryes-Kirilov, Joseph Wolanski, Keith Dunaway, Ayokunmi Ajetunmobi, Victor Dillard:
Erratum to: Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments. 202:1 - Nathan K. Schaefer, Beth Shapiro, Richard E. Green:
AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data. 203:1-203:22 - Ergude Bao, Lingxiao Lan:
HALC: High throughput algorithm for long read error correction. 204:1-204:12 - Garrett W. Birkel, Amit Ghosh, Vinay Satish Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling, Héctor García Martín:
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. 205:1-205:11 - Jia-Feng Yu, Xianghua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou, Ji-Hua Wang:
DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins. 206:1-206:5 - William W. Greenwald, He Li, Erin N. Smith, Paola Benaglio, Naoki Nariai, Kelly A. Frazer:
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data. 207:1-207:6 - Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani, Abdoulaye Baniré Diallo:
A machine learning approach for viral genome classification. 208:1-208:11 - Rasha E. Boulos, Nicolas Tremblay, Alain Arneodo, Pierre Borgnat, Benjamin Audit:
Multi-scale structural community organisation of the human genome. 209:1-209:13 - Putri W. Novianti, Victor L. Jong, Kit C. B. Roes, Marinus J. C. Eijkemans:
Meta-analysis approach as a gene selection method in class prediction: does it improve model performance? A case study in acute myeloid leukemia. 210:1-210:11 - Ji-Hye Choi, Seong-Eui Hong, Hyun Goo Woo:
Pan-cancer analysis of systematic batch effects on somatic sequence variations. 211:1-211:10 - Guifang Fu, Gang Wang, Xiaotian Dai:
An adaptive threshold determination method of feature screening for genomic selection. 212:1-212:10 - Clare Pacini, James W. Ajioka, Gos Micklem:
Empirical Bayes method for reducing false discovery rates of correlation matrices with block diagonal structure. 213:1-213:6 - Peter Kamp Busk, Bo Pilgaard, Mateusz Jakub Lezyk, Sharon A. Meyer, Lene Lange:
Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function. 214:1-214:9 - Ebrahim Afyounian, Matti Annala, Matti Nykter:
Segmentum: a tool for copy number analysis of cancer genomes. 215:1-215:10 - Akhilesh Kaushal, Hongmei Zhang, Wilfried Karmaus, Meredith Ray, Mylin A. Torres, Alicia K. Smith, Shu-Li Wang:
Comparison of different cell type correction methods for genome-scale epigenetics studies. 216:1-216:12 - Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C. Elston, Bong-Jo Kim, Sungho Won:
On the association analysis of CNV data: a fast and robust family-based association method. 217:1-217:11 - Sarvesh Nikumbh, Nico Pfeifer:
Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization. 218:1-218:16 - Garrett W. Birkel, Amit Ghosh, Vinay Satish Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling, Héctor García Martín:
Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. 219:1-219:2 - Tanchanok Wisitponchai, Watshara Shoombuatong, Vannajan Sanghiran Lee, Kuntida Kitidee, Chatchai Tayapiwatana:
AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking. 220:1-220:12 - Mark D. Temple:
An auditory display tool for DNA sequence analysis. 221:1-221:11 - Alencar Xavier, Shizhong Xu, William M. Muir, Katy Martin Rainey:
Erratum to: Genomic prediction using subsampling. 222:1 - You-Yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen, Hurng-Yi Wang:
De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline. 223:1-223:10 - Debangana Chakravorty, Tanmoy Jana, Sukhen Das Mandal, Anuradha Seth, Anubrata Bhattacharya, Sudipto Saha:
MYCbase: a database of functional sites and biochemical properties of Myc in both normal and cancer cells. 224:1-224:10 - Loris Bertoldi, Claudio Forcato, Nicola Vitulo, Giovanni Birolo, Fabio De Pascale, Erika Feltrin, Riccardo Schiavon, Franca Anglani, Susanna Negrisolo, Alessandra Zanetti, Francesca D'Avanzo, Rosella Tomanin, Georgine Faulkner, Alessandro Vezzi, Giorgio Valle:
QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. 225:1-225:11 - Mohammed Al-Jaff, Eric Sandström, Manfred G. Grabherr:
microTaboo: a general and practical solution to the k-disjoint problem. 228:1-228:7 - Li Chen, Yuxi Lian, Yi Guo, Yuanyuan Wang, Thomas S. Hatsukami, Kristi Pimentel, Niranjan Balu, Chun Yuan:
A vascular image registration method based on network structure and circuit simulation. 229:1-229:13 - Irene Epifanio:
Intervention in prediction measure: a new approach to assessing variable importance for random forests. 230:1-230:16 - Francisco Avila Cobos, Jasper Anckaert, Pieter-Jan Volders, Celine Everaert, Dries Rombaut, Jo Vandesompele, Katleen De Preter, Pieter Mestdagh:
Zipper plot: visualizing transcriptional activity of genomic regions. 231:1-231:9 - Jochen Kruppa, Klaus Jung:
Automated multigroup outlier identification in molecular high-throughput data using bagplots and gemplots. 232:1-232:10 - Bertjan Broeksema, Magdalena Calusinska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse, Mohammad Ghoniem:
ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins. 233:1-233:12 - Lianbo Yu, Soledad Fernandez, Guy N. Brock:
Power analysis for RNA-Seq differential expression studies. 234:1-234:9 - Liang Sun, Yongnan Zhu, A. S. M. Ashique Mahmood, Catalina O. Tudor, Jia Ren, K. Vijay-Shanker, Jian Chen, Carl J. Schmidt:
WebGIVI: a web-based gene enrichment analysis and visualization tool. 237:1-237:10 - Jose Cleydson F. Silva, Thales Francisco Mota Carvalho, Marcos F. Basso, Michihito Deguchi, Welison A. Pereira, Roberto R. Sobrinho, Pedro M. P. Vidigal, Otávio J. B. Brustolini, Fabyano F. Silva, Maximiller Dal-Bianco, Renildes L. F. Fontes, Anésia A. Santos, Francisco Murilo Zerbini, Fabio Ribeiro Cerqueira, Elizabeth P. B. Fontes:
Geminivirus data warehouse: a database enriched with machine learning approaches. 240:1-240:11 - Jing Liu, Yaxiong Chi, Chen Zhu, Yaochu Jin:
A time series driven decomposed evolutionary optimization approach for reconstructing large-scale gene regulatory networks based on fuzzy cognitive maps. 241:1-241:14 - Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer, Oliver Kohlbacher:
ImmunoNodes - graphical development of complex immunoinformatics workflows. 242:1-242:7 - Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li:
Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. 243:1-243:12 - Andrea Tangherloni, Marco S. Nobile, Daniela Besozzi, Giancarlo Mauri, Paolo Cazzaniga:
LASSIE: simulating large-scale models of biochemical systems on GPUs. 246 - Xiang Gao, Huaiying Lin, Kashi Vishwanath Revanna, Qunfeng Dong:
A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy. 247:1-247:10 - Miles Aron, Richard J. Browning, Dario Carugo, Erdinc Sezgin, Jorge Bernardino de la Serna, Christian Eggeling, Eleanor Stride:
Spectral imaging toolbox: segmentation, hyperstack reconstruction, and batch processing of spectral images for the determination of cell and model membrane lipid order. 254 - Ian H. Holmes:
Solving the master equation for Indels. 255:1-255:10 - Joanna Zyla, Michal Marczyk, January 3rd Weiner, Joanna Polanska:
Ranking metrics in gene set enrichment analysis: do they matter? 256:1-256:12 - Surabhi Maheshwari, Michal Brylinski:
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks. 257:1-257:14 - Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim, Jongsun Jung:
HLAscan: genotyping of the HLA region using next-generation sequencing data. 258:1-258:11 - Mohamed-Ashick M. Saleem, Marco-Antonio Mendoza-Parra, Pierre-Etienne Cholley, Matthias Blum, Hinrich Gronemeyer:
Epimetheus - a multi-profile normalizer for epigenomic sequencing data. 259:1-259:9 - Moritz Hanke, Ronja Foraita:
Clone temporal centrality measures for incomplete sequences of graph snapshots. 261:1-261:18 - Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hao Hong, Xiaochen Bo, Fei Li:
NFPscanner: a webtool for knowledge-based deciphering of biomedical networks. 262:1-262:9 - Knut D. Rand, Ivar Grytten, Alexander Johan Nederbragt, Geir Storvik, Ingrid Kristine Glad, Geir Kjetil Sandve:
Coordinates and intervals in graph-based reference genomes. 263:1-263:8 - Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig, Geir Kjetil Sandve:
The rainfall plot: its motivation, characteristics and pitfalls. 264:1-264:11 - Hamzah Syed, Andrea L. Jorgensen, Andrew P. Morris:
SurvivalGWAS_SV: software for the analysis of genome-wide association studies of imputed genotypes with "time-to-event" outcomes. 265:1-265:6 - Anna Kusnezowa, Lars I. Leichert:
In silico approach to designing rational metagenomic libraries for functional studies. 267:1-267:11 - Zhen Zhang, Shumin Xia, Pakorn Kanchanawong:
An integrated enhancement and reconstruction strategy for the quantitative extraction of actin stress fibers from fluorescence micrographs. 268:1-268:14 - Zhenqing Ye, Tao Ma, Michael Kalmbach, Surendra Dasari, Jean-Pierre A. Kocher, Liguo Wang:
CircularLogo: A lightweight web application to visualize intra-motif dependencies. 269:1-269:8 - Zhuo Wang, Shuilin Jin, Guiyou Liu, Xiurui Zhang, Nan Wang, Deliang Wu, Yang Hu, Chiping Zhang, Qinghua Jiang, Li Xu, Yadong Wang:
DTWscore: differential expression and cell clustering analysis for time-series single-cell RNA-seq data. 270:1-270:14 - Charles C. David, Ettayapuram Ramaprasad Azhagiya Singam, Donald J. Jacobs:
JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories. 271:1-271:9 - Jakob Unger, Mike Mansour, Marcin Kopaczka, Nina Gronloh, Marc Spehr, Dorit Merhof:
An unsupervised learning approach for tracking mice in an enclosed area. 272:1-272:14 - Marijke Van Moerbeke, Adetayo Kasim, Willem Talloen, Joke Reumers, Hinrich W. H. Göhlmann, Ziv Shkedy:
A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays. 273:1-273:14 - Florian Kandlinger, Maximilian G. Plach, Rainer Merkl:
AGeNNT: annotation of enzyme families by means of refined neighborhood networks. 274:1-274:13 - Xiaoyang Jing, Qiwen Dong:
MQAPRank: improved global protein model quality assessment by learning-to-rank. 275:1-275:8 - Spela Baebler, Miha Svalina, Marko Petek, Katja Stare, Ana Rotter, Marusa Pompe-Novak, Kristina Gruden:
quantGenius: implementation of a decision support system for qPCR-based gene quantification. 276:1-276:11 - Tanlin Sun, Bo Zhou, Luhua Lai, Jianfeng Pei:
Sequence-based prediction of protein protein interaction using a deep-learning algorithm. 277:1-277:8 - Kazuhiro Takemoto, Kazuki Aie:
Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions. 278:1-278:9 - Dmitry Y. Mozzherin, Alexander A. Myltsev, David J. Patterson:
"gnparser": a powerful parser for scientific names based on Parsing Expression Grammar. 279:1-279:14 - Yong Wan, Hideo Otsuna, Holly A. Holman, Brig Bagley, Masayoshi Ito, A. Kelsey Lewis, Mary Colasanto, Gabrielle Kardon, Kei Ito, Charles D. Hansen:
FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis. 280:1-280:15 - Yan Xu, Zhipeng Jia, Liang-Bo Wang, Yuqing Ai, Fang Zhang, Maode Lai, Eric I-Chao Chang:
Large scale tissue histopathology image classification, segmentation, and visualization via deep convolutional activation features. 281:1-281:17 - Boris Shabash, Kay C. Wiese:
Numerical integration methods and layout improvements in the context of dynamic RNA visualization. 282:1-282:18 - Jonathan Louis Golob, Elisa Margolis, Noah G. Hoffman, David N. Fredricks:
Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities. 283:1-283:12 - Christian Schäfer, Alexander H. Schmidt, Jürgen Sauter:
Hapl-o-Mat: open-source software for HLA haplotype frequency estimation from ambiguous and heterogeneous data. 284:1-284:10 - Lukasz Wróbel, Adam Gudys, Marek Sikora:
Learning rule sets from survival data. 285:1-285:13 - Fatima Zare, Michelle Dow, Nicholas Monteleone, Abdelrahman Hosny, Sheida Nabavi:
An evaluation of copy number variation detection tools for cancer using whole exome sequencing data. 286:1-286:13 - Aziz Khan, Anthony Mathelier:
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. 287:1-287:8 - Toshiyuki Oda, Kyungtaek Lim, Kentaro Tomii:
Simple adjustment of the sequence weight algorithm remarkably enhances PSI-BLAST performance. 288 - Kazunori D. Yamada, Satoshi Omori, Hafumi Nishi, Masaru Miyagi:
Identification of the sequence determinants of protein N-terminal acetylation through a decision tree approach. 289 - Marek Palkowski, Wlodzimierz Bielecki:
Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing. 290 - Miha Stajdohar, Rafael D. Rosengarten, Janez Kokosar, Luka Jeran, Domen Blenkus, Gad Shaulsky, Blaz Zupan:
dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond. 291 - Jennifer Rogers, Andrew Fishberg, Nora Youngs, Yi-Chieh Wu:
Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species. 292 - Frank Keul, Martin Hess, Michael Goesele, Kay Hamacher:
PFASUM: a substitution matrix from Pfam structural alignments. 293 - Jian Zhang, Haiting Chai, Guifu Yang, Zhiqiang Ma:
Prediction of bioluminescent proteins by using sequence-derived features and lineage-specific scheme. 294 - Atif Ali Khan, Dejan Katanic, Juilee Thakar:
Meta-analysis of cell- specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes. 295 - Alex M. Ascensión, Mikel Arrospide-Elgarresta, Ander Izeta, Marcos J. Araúzo-Bravo:
NaviSE: superenhancer navigator integrating epigenomics signal algebra. 296 - Pei Fen Kuan, R. Scott Powers, Shuyao He, Kaiqiao Li, Xiaoyu Zhao, Bo Huang:
A systematic evaluation of nucleotide properties for CRISPR sgRNA design. 297 - Shermin Pei, Betty L. Slinger, Michelle M. Meyer:
Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15. 298 - Thomas M. Poulsen, Martin C. Frith:
Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads. 299 - Wei Wang, Lin Sun, Shiguang Zhang, Hongjun Zhang, Jinling Shi, Tianhe Xu, Keliang Li:
Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences. 300 - Stephen J. Bush, Mary E. B. McCulloch, Kim M. Summers, David A. Hume, Emily L. Clark:
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries. 301 - Wen Torng, Russ B. Altman:
3D deep convolutional neural networks for amino acid environment similarity analysis. 302 - Kolja Stahl, Michael Schneider, Oliver Brock:
EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction. 303 - Reiko Nishihara, Kimberly Glass, Kosuke Mima, Tsuyoshi Hamada, Jonathan A. Nowak, Zhi Rong Qian, Peter Kraft, Edward L. Giovannucci, Charles S. Fuchs, Andrew T. Chan, John Quackenbush, Shuji Ogino, Jukka-Pekka Onnela:
Biomarker correlation network in colorectal carcinoma by tumor anatomic location. 304 - Atul Kamboj, Claus V. Hallwirth, Ian E. Alexander, Geoffrey B. McCowage, Belinda Kramer:
Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data. 305 - Ahmet Rasit Ozturk, Tolga Can:
A multiplex primer design algorithm for target amplification of continuous genomic regions. 306 - Yusuke Azuma, Shuichi Onami:
Biologically constrained optimization based cell membrane segmentation in C. elegans embryos. 307 - Katsuhiro Omae, Osamu Komori, Shinto Eguchi:
Quasi-linear score for capturing heterogeneous structure in biomarkers. 308 - Xiting Yan, Anqi Liang, Jose Gomez, Lauren Cohn, Hongyu Zhao, Geoffrey Lowell Chupp:
A novel pathway-based distance score enhances assessment of disease heterogeneity in gene expression. 309 - Kai Battenberg, Ernest K. Lee, Joanna C. Chiu, Alison M. Berry, Daniel Potter:
OrthoReD: a rapid and accurate orthology prediction tool with low computational requirement. 310 - Andrew Bartlett, Bart Penders, Jamie Lewis:
Bioinformatics: indispensable, yet hidden in plain sight? 311 - J. F. Mudge, Christopher J. Martyniuk, J. E. Houlahan:
Optimal alpha reduces error rates in gene expression studies: a meta-analysis approach. 312 - Sirajul Salekin, Mehrab Ghanat Bari, Itay Raphael, Thomas G. Forsthuber, Jianqiu (Michelle) Zhang:
Early response index: a statistic to discover potential early stage disease biomarkers. 313 - Sascha Schäuble, Anne-Kristin Stavrum, Mathias Bockwoldt, Pål Puntervoll, Ines Heiland:
SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. 314 - Xi Chen, Chen Wang, Shanjiang Tang, Ce Yu, Quan Zou:
CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment. 315 - Giorgos Minas, Hiroshi Momiji, Dafyd J. Jenkins, Maria J. Costa, David A. Rand, Bärbel Finkenstädt:
ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data. 316 - Michael I. Klein, David F. Stern, Hongyu Zhao:
GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles. 317 - Marcelo Rodrigo de Castro, Catherine dos Santos Tostes, Alberto M. R. Dávila, Hermes Senger, Fabrício Alves Barbosa da Silva:
SparkBLAST: scalable BLAST processing using in-memory operations. 318 - Sheng Yang Michael Loh, Yoshitaka Ogawa, Sara Kawana, Koichiro Tamura, Hwee Kuan Lee:
Semi-automated quantitative Drosophila wings measurements. 319 - Hasan Awad Aljohi, Wanfei Liu, Qiang Lin, Jun Yu, Songnian Hu:
ISVASE: identification of sequence variant associated with splicing event using RNA-seq data. 320 - Valerio Orlandini, Aldesia Provenzano, Sabrina Giglio, Alberto Magi:
SLMSuite: a suite of algorithms for segmenting genomic profiles. 321 - Nicola Lazzarini, Jaume Bacardit:
RGIFE: a ranked guided iterative feature elimination heuristic for the identification of biomarkers. 322 - Yuxuan Yuan, Philipp E. Bayer, Armin Scheben, Chon-Kit Kenneth Chan, David Edwards:
BioNanoAnalyst: a visualisation tool to assess genome assembly quality using BioNano data. 323 - Axel Wedemeyer, Lasse Kliemann, Anand Srivastav, Christian Schielke, Thorsten B. Reusch, Philip Rosenstiel:
An improved filtering algorithm for big read datasets and its application to single-cell assembly. 324 - Shailesh Tripathi, Jason Lloyd-Price, Andre S. Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib:
sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters. 325 - Lili Zhao, Mark T. Anderson, Weisheng Wu, Harry L. T. Mobley, Michael A. Bachman:
TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. 326 - Hongrui Wang, Hongwei Liu, Leixin Cai, Caixia Wang, Qiang Lv:
Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking. 327 - Mustafa Alshawaqfeh, Ahmad Bashaireh, Erchin Serpedin, Jan Suchodolski:
Reliable Biomarker discovery from Metagenomic data via RegLRSD algorithm. 328 - Yadav Kuleesha, Feng Lin, Martin Wasser:
Spatial pattern analysis of nuclear migration in remodelled muscles during Drosophila metamorphosis. 329 - Dianhao Guo, Jiapeng Luo, Yuenan Zhou, Huamei Xiao, Kang He, Chuanlin Yin, Jianhua Xu, Fei Li:
ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data. 330 - Jeremy P. Koelmel, Nicholas M. Kroeger, Candice Z. Ulmer, John A. Bowden, Rainey E. Patterson, Jason A. Cochran, Christopher W. Beecher, Timothy J. Garrett, Richard A. Yost:
LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. 331 - Ziyi Li, Sandra E. Safo, Qi Long:
Incorporating biological information in sparse principal component analysis with application to genomic data. 332 - Eleni Ioanna Delatola, Emilie Lebarbier, Tristan Mary-Huard, François Radvanyi, Stéphane Robin, Jennifer Wong:
SegCorr a statistical procedure for the detection of genomic regions of correlated expression. 333 - Marc Jeanmougin, Josselin Noirel, Cédric Coulonges, Jean-François Zagury:
HLA-check: evaluating HLA data from SNP information. 334 - Sheng Zhang, Bo Wang, Lin Wan, Lei M. Li:
Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling. 335 - Su Hee Chu, Yen-Tsung Huang:
Integrated genomic analysis of biological gene sets with applications in lung cancer prognosis. 336 - Sehrish Kanwal, Farah Zaib Khan, Andrew Lonie, Richard O. Sinnott:
Investigating reproducibility and tracking provenance - A genomic workflow case study. 337 - Ksenia Khelik, Karin Lagesen, Geir Kjetil Sandve, Torbjørn Rognes, Alexander Johan Nederbragt:
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. 338 - Bogumil Konopka, Marta Marciniak, Witold Dyrka:
Quantiprot - a Python package for quantitative analysis of protein sequences. 339 - Sara González-Pérez, Florencio Pazos, Monica Chagoyen:
Factors affecting interactome-based prediction of human genes associated with clinical signs. 340 - John Alexander, Dimitris Mantzaris, Marianthi Georgitsi, Petros Drineas, Peristera Paschou:
Variant Ranker: a web-tool to rank genomic data according to functional significance. 341 - Alvin Farrel, Jun-tao Guo:
An efficient algorithm for improving structure-based prediction of transcription factor binding sites. 342 - Jie Liu, Minyi Su, Zhihai Liu, Jie Li, Yan Li, Renxiao Wang:
Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints. 343 - Sharon Marie Lutz, Annie Thwing, Sarah Schmiege, Miranda Kroehl, Christopher D. Baker, Anne P. Starling, John E. Hokanson, Debashis Ghosh:
Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications. 344 - Se-Ran Jun, Intawat Nookaew, Loren J. Hauser, Andrey Gorin:
Assessment of genome annotation using gene function similarity within the gene neighborhood. 345 - Jan Schröder, Adrianto Wirawan, Bertil Schmidt, Anthony T. Papenfuss:
CLOVE: classification of genomic fusions into structural variation events. 346 - Tamás Nagy, Martin Kampmann:
CRISPulator: a discrete simulation tool for pooled genetic screens. 347 - Yanan Zhu, Qi Ouyang, Youdong Mao:
A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy. 348 - Yasser B. Ruiz-Blanco, Guillermín Agüero-Chapín, Enrique García-Hernández, Orlando Álvarez, Agostinho Antunes, James Green:
Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone. 349 - Guoxian Yu, Chang Lu, Jun Wang:
NoGOA: predicting noisy GO annotations using evidences and sparse representation. 350 - Jennifer A. Tom, Jens Reeder, William F. Forrest, Robert R. Graham, Julie Hunkapiller, Timothy W. Behrens, Tushar R. Bhangale:
Identifying and mitigating batch effects in whole genome sequencing data. 351 - Antoine Basset, Patrick Bouthemy, Jérôme Boulanger, François Waharte, Jean Salamero, Charles Kervrann:
An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images. 352 - Syafiq Kamarul Azman, Muhammad Zohaib Anwar, Andreas Henschel:
Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture. 353 - James E. Barrett, Andrew Feber, Javier Herrero, Miljana Tanic, Gareth A. Wilson, Charles Swanton, Stephan Beck:
Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection. 354 - Sheng Liu, Cristina Zibetti, Jun Wan, Guohua Wang, Seth Blackshaw, Jiang Qian:
Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility. 355 - Zhao Li, Jin Li, Peng Yu:
l1kdeconv: an R package for peak calling analysis with LINCS L1000 data. 356 - Jeremy R. Wang, Bryan Quach, Terrence S. Furey:
Correcting nucleotide-specific biases in high-throughput sequencing data. 357 - Katrin Hainke, Sebastian Szugat, Roland Fried, Jörg Rahnenführer:
Variable selection for disease progression models: methods for oncogenetic trees and application to cancer and HIV. 358 - Daniel Amsel, Andreas Vilcinskas, André Billion:
Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum. 359 - Yan Xu, Yeshu Li, Zhengyang Shen, Ziwei Wu, Teng Gao, Yubo Fan, Maode Lai, Eric I-Chao Chang:
Parallel multiple instance learning for extremely large histopathology image analysis. 360 - Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram, John Pestian:
A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support. 361 - Gregory J. Zynda, Jawon Song, Lorenzo Concia, Emily E. Wear, Linda Hanley-Bowdoin, William F. Thompson, Matthew W. Vaughn:
Repliscan: a tool for classifying replication timing regions. 362 - Carlos Guzman, Iván D'Orso:
CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction. 363 - Alejandro Sune-Aunon, Álvaro Jorge-Peñas, Rocío Aguilar-Cuenca, Miguel Vicente-Manzanares, Hans Van Oosterwyck, Arrate Muñoz-Barrutia:
Full L1-regularized Traction Force Microscopy over whole cells. 365 - Guoshuai Cai, Shoudan Liang, Xiaofeng Zheng, Feifei Xiao:
Local sequence and sequencing depth dependent accuracy of RNA-seq reads. 364:1-364:12 - Lisa Katharina Blaß, Christian Weyler, Elmar Heinzle:
Network design and analysis for multi-enzyme biocatalysis. 366:1-366:12 - Joseph Guhlin, Kevin A. T. Silverstein, Peng Zhou, Peter Tiffin, Nevin D. Young:
ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding. 367:1-367:8 - Gamal K. O. Crichton, Sampo Pyysalo, Billy Chiu, Anna Korhonen:
A neural network multi-task learning approach to biomedical named entity recognition. 368:1-368:14 - Olivier Sheik Amamuddy, Nigel Bishop, Özlem Tastan Bishop:
Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks. 369:1-369:7 - Seirana Hashemi, Abbas Nowzari-Dalini, Adrin Jalali, Ali Mohammad Banaei-Moghaddam, Zahra Razaghi Moghadam Kashani:
Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains. 370:1-370:18 - Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch, Dominik Heider:
eccCL: parallelized GPU implementation of Ensemble Classifier Chains. 371:1-371:4 - K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer, Lawrence E. Hunter:
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles. 372:1-372:14 - Manuel Rueda, Ali Torkamani:
SG-ADVISER mtDNA: a web server for mitochondrial DNA annotation with data from 200 samples of a healthy aging cohort. 373:1-373:10 - Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier:
Evaluation of the impact of Illumina error correction tools on de novo genome assembly. 374:1-374:13 - Xin-Ping Xie, Yu-Feng Xie, Hong-Qiang Wang:
A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification. 375 - James J. Yang, L. Keoki Williams, Anne Buu:
Identifying pleiotropic genes in genome-wide association studies from related subjects using the linear mixed model and Fisher combination function. 376 - Saghi Nojoomi, Patrice Koehl:
A weighted string kernel for protein fold recognition. 378 - Jiyun Zhou, Qin Lu, Ruifeng Xu, Yulan He, Hongpeng Wang:
EL_PSSM-RT: DNA-binding residue prediction by integrating ensemble learning with PSSM Relation Transformation. 379 - Badri Adhikari, Jianlin Cheng:
Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts. 380 - Lian Liu, Shao-Wu Zhang, Yufei Huang, Jia Meng:
QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model. 387:1-387:12 - Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun, Qingling Zhang:
Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer. 388 - Suyeon Kang, Jongwoo Song:
Robust gene selection methods using weighting schemes for microarray data analysis. 389:1-389:15 - John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V. Santana-Quintero, Upendra Katneni, Vahan Simonyan, Chava Kimchi-Sarfaty:
A new and updated resource for codon usage tables. 391:1-391:10 - Xiaoyang Jing, Qiwen Dong, Ruqian Lu:
RRCRank: a fusion method using rank strategy for residue-residue contact prediction. 390 - Gabriella Sferra, Federica Fratini, Marta Ponzi, Elisabetta Pizzi:
Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling. 396:1-396:7 - Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Spiros Skiadopoulos, Theodore Dalamagas:
BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets. 399:1-399:8 - Steve Lefever, Filip Pattyn, Bram De Wilde, Frauke Coppieters, Sarah De Keulenaer, Jan Hellemans, Jo Vandesompele:
High-throughput PCR assay design for targeted resequencing using primerXL. 400:1-400:9 - Jared Ostmeyer, Scott Christley, William Rounds, Inimary T. Toby, Benjamin M. Greenberg, Nancy Monson, Lindsay G. Cowell:
Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis. 401:1-401:10 - Michael Kern, Alexander Lex, Nils Gehlenborg, Chris R. Johnson:
Interactive visual exploration and refinement of cluster assignments. 406 - Matthias Zytnicki:
mmquant: how to count multi-mapping reads? 411:1-411:6 - Mengdi Zhao, Jie An, Haiwen Li, Jiazhi Zhang, Shang-Tong Li, Xue-Mei Li, Meng-Qiu Dong, Heng Mao, Louis Tao:
Segmentation and classification of two-channel C. elegans nucleus-labeled fluorescence images. 412:1-412:13 - Wei Hu, Amrapali Zaveri, Honglei Qiu, Michel Dumontier:
Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata. 415:1-415:12 - Thomas J. Hardcastle:
Methods for discovering genomic loci exhibiting complex patterns of differential methylation. 416:1-416:11 - Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu, Jianlin Cheng:
Deep learning methods for protein torsion angle prediction. 417:1-417:13 - José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves, Pablo Marín-García, Ignacio Medina, Vicente Arnau, Joaquín Dopazo:
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy. 421:1-421:5 - Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun:
Improving contig binning of metagenomic data using (d2S) oligonucleotide frequency dissimilarity. 425:1-425:14 - Duo Xu, Yousef Jaber, Pavlos Pavlidis, Omer Gokcumen:
VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. 426:1-426:8 - Jerome Audoux, Mikaël Salson, Christophe F. Grosset, Sacha Beaumeunier, Jean-Marc Holder, Therese Commes, Nicolas Philippe:
SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines. 428:1-428:14 - Sophie Molnos, Clemens Baumbach, Simone Wahl, Martina Müller-Nurasyid, Konstantin Strauch, Rui Wang-Sattler, Melanie Waldenberger, Thomas Meitinger, Jerzy Adamski, Gabi Kastenmüller, Karsten Suhre, Annette Peters, Harald Grallert, Fabian J. Theis, Christian Gieger:
pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms. 429:1-429:8 - Juan Carlos Aledo, Francisco R. Cantón, Francisco J. Veredas:
A machine learning approach for predicting methionine oxidation sites. 430:1-430:14 - Jose Cleydson F. Silva, Thales Francisco Mota Carvalho, Elizabeth P. B. Fontes, Fabio Ribeiro Cerqueira:
Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae. 431:1-431:14 - Maninder Sandhu, V. Sureshkumar, Chandra Prakash, Rekha Dixit, Amolkumar U. Solanke, Tilak Raj Sharma, Trilochan Mohapatra, Amitha Mithra S. V.:
RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. 432:1-432:11 - Alan Beccati, Jan Gerken, Christian Quast, Pelin Yilmaz, Frank Oliver Glöckner:
SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees. 433:1-433:4 - Peng Zhai, Longshu Yang, Xiao Guo, Zhe Wang, Jiangtao Guo, Xiaoqi Wang, Huaiqiu Zhu:
MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics. 434:1-434:16 - Nazar Zaki, Chandana Tennakoon:
BioCarian: search engine for exploratory searches in heterogeneous biological databases. 435:1-435:15 - Jianing Gao, Changlin Wan, Huan Zhang, Ao Li, Qiguang Zang, Rongjun Ban, Asim Ali, Zhenghua Yu, Qinghua Shi, Xiaohua Jiang, Yuanwei Zhang:
Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data. 436:1-436:6 - Joseph N. Paulson, Cho-Yi Chen, Camila Miranda Lopes-Ramos, Marieke L. Kuijjer, John Platig, Abhijeet R. Sonawane, Maud Fagny, Kimberly Glass, John Quackenbush:
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. 437:1-437:10 - Enfeng Qi, Dongyu Wang, Bo Gao, Yang Li, Guojun Li:
Block-based characterization of protease specificity from substrate sequence profile. 438:1-438:9 - Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou, Kui Lin:
Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family. 439:1-439:8 - Bence Bolgár, Peter Antal:
VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization. 440:1-440:18 - A. Eck, Luisa M. Zintgraf, E. F. J. de Groot, Tim G. J. de Meij, Taco S. Cohen, P. H. M. Savelkoul, Max Welling, A. E. Budding:
Interpretation of microbiota-based diagnostics by explaining individual classifier decisions. 441:1-441:13 - Michael Ferlaino, Mark F. Rogers, Hashem A. Shihab, Matthew E. Mort, David N. Cooper, Tom R. Gaunt, Colin Campbell:
An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome. 442:1-442:8 - Shumin Li, Junjie Chen, Bin Liu:
Protein remote homology detection based on bidirectional long short-term memory. 443:1-443:8 - Sebastian Proost, Agnieszka Krawczyk, Marek Mutwil:
LSTrAP: efficiently combining RNA sequencing data into co-expression networks. 444:1-444:9 - Wei Zheng, Hongfei Lin, Ling Luo, Zhehuan Zhao, Zhengguang Li, Yijia Zhang, Zhihao Yang, Jian Wang:
An attention-based effective neural model for drug-drug interactions extraction. 445:1-445:11 - Maria Taboada, Hadriana Rodríguez, Ranga Chandra Gudivada, Diego Martínez Hernández:
A new synonym-substitution method to enrich the human phenotype ontology. 446:1-446:12 - Xue Jiang, Han Zhang, Feng Duan, Xiongwen Quan:
Identify Huntington's disease associated genes based on restricted Boltzmann machine with RNA-seq data. 447:1-447:13 - Scott Christley, Mikhail K. Levin, Inimary T. Toby, John M. Fonner, Nancy Monson, William Rounds, Florian Rubelt, Walter Scarborough, Richard H. Scheuermann, Lindsay G. Cowell:
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. 448:1-448:5 - Marco Notaro, Max Schubach, Peter N. Robinson, Giorgio Valentini:
Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods. 449:1-449:18 - Jaehee Kim, Haseong Kim:
Partitioning of functional gene expression data using principal points. 450:1-450:17 - Hyejin Cho, Wonjun Choi, Hyunju Lee:
A method for named entity normalization in biomedical articles: application to diseases and plants. 451:1-451:12 - Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao, Yunping Zhu:
LiverWiki: a wiki-based database for human liver. 452:1-452:11 - Chenggang Yu, Hyung Jun Woo, Xueping Yu, Tatsuya Oyama, Anders Wallqvist, Jaques Reifman:
A strategy for evaluating pathway analysis methods. 453:1-453:11 - Youyi Fong, Ying Huang, Peter B. Gilbert, Sallie R. Permar:
chngpt: threshold regression model estimation and inference. 454:1-454:7 - Chaitanya R. Acharya, Kouros Owzar, Andrew S. Allen:
Mapping eQTL by leveraging multiple tissues and DNA methylation. 455 - Jakub Wiedemann, Tomasz Zok, Maciej Milostan, Marta Szachniuk:
LCS-TA to identify similar fragments in RNA 3D structures. 456 - R. Greg Stacey, Michael A. Skinnider, Nichollas E. Scott, Leonard J. Foster:
A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE). 457 - Yahya Bokhari, Tomasz Arodz:
QuaDMutEx: quadratic driver mutation explorer. 458 - Jia Wen, Jue Wang, Qing Zhang, Dianjing Guo:
A heuristic model for computational prediction of human branch point sequence. 459 - Biswanath Chowdhury, Arnav Garai, Gautam Garai:
An optimized approach for annotation of large eukaryotic genomic sequences using genetic algorithm. 460 - Oana Carja, Tongji Xing, Edward W. J. Wallace, Joshua B. Plotkin, Premal Shah:
riboviz: analysis and visualization of ribosome profiling datasets. 461 - Yiwei Li, Lucian Ilie:
SPRINT: ultrafast protein-protein interaction prediction of the entire human interactome. 485:1-485:11 - Levi D. McClenny, Mahdi Imani, Ulisses M. Braga-Neto:
BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems. 519:1-519:8 - Giulio Spinozzi, Andrea Calabria, Stefano Brasca, Stefano Beretta, Ivan Merelli, Luciano Milanesi, Eugenio Montini:
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites. 520:1-520:12 - Mike Myschyshyn, Marco Farren-Dai, Tien-Jui Chuang, David Vocadlo:
Software for rapid time dependent ChIP-sequencing analysis (TDCA). 521:1-521:16 - Megan J. Bowman, Jane A. Pulman, Tiffany L. Liu, Kevin L. Childs:
A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa. 522:1-522:15 - Yao-Ting Huang, Yu-Wen Huang:
An efficient error correction algorithm using FM-index. 524:1-524:9 - Wael Karain:
Detecting transitions in protein dynamics using a recurrence quantification analysis based bootstrap method. 525:1-525:13 - Peter Bajcsy, Soweon Yoon, Stephen J. Florczyk, Nathan Hotaling, Mylene Simon, Piotr M. Szczypinski, Nicholas Schaub, Carl G. Simon, Mary Brady, Ram D. Sriram:
Modeling, validation and verification of three-dimensional cell-scaffold contacts from terabyte-sized images. 526:1-526:23 - Qinxue Meng, Daniel R. Catchpoole, David B. Skillicorn, Paul J. Kennedy:
DBNorm: normalizing high-density oligonucleotide microarray data based on distributions. 527:1-527:11 - John M. Gaspar, Ronald P. Hart:
DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data. 528:1-528:8 - Curtis T. Rueden, Johannes E. Schindelin, Mark C. Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena, Kevin W. Eliceiri:
ImageJ2: ImageJ for the next generation of scientific image data. 529:1-529:26 - Maxwell T. Spadafore, Kayvan Najarian, Alan P. Boyle:
A proximity-based graph clustering method for the identification and application of transcription factor clusters. 530:1-530:14 - Jelena Calyseva, Mauno Vihinen:
PON-SC - program for identifying steric clashes caused by amino acid substitutions. 531:1-531:8 - Janna L. Fierst, Duncan A. Murdock:
Decontaminating eukaryotic genome assemblies with machine learning. 533:1-533:16 - Michael T. Ganger, Geoffrey D. Dietz, Sarah J. Ewing:
A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments. 534:1-534:11 - Bart Broeckx, Luc Peelman, Jimmy Saunders, Dieter Deforce, Lieven Clement:
Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations. 535:1-535:10 - Vahid Jalili, Matteo Matteucci, Marco Masseroli, Stefano Ceri:
Explorative visual analytics on interval-based genomic data and their metadata. 536:1-536:15 - Vassily A. Lyubetsky, Roman Gershgorin, Konstantin Yu. Gorbunov:
Chromosome structures: reduction of certain problems with unequal gene content and gene paralogs to integer linear programming. 537:1-537:18 - Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol, Gregory M. Bonito:
CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences. 538:1-538:9 - Kang K. Yan, Hongyu Zhao, Herbert Pang:
A comparison of graph- and kernel-based -omics data integration algorithms for classifying complex traits. 539:1-539:13 - Ralph W. Crosby, Tiffani L. Williams:
Fast algorithms for computing phylogenetic divergence time. 514:1-514:13 - Oyetunji E. Ogundijo, Xiaodong Wang:
Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach. 541:1-541:15 - Yuangen Yao, Rong Gui, Quan Liu, Ming Yi, Haiyou Deng:
Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction. 542:1-542:12 - Carlos Ruiz-Arenas, Juan R. González:
Redundancy analysis allows improved detection of methylation changes in large genomic regions. 553:1-553:9 - Matthias Beyens, Nele Boeckx, Guy Van Camp, Ken Op de Beeck, Geert Vandeweyer:
pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data. 554:1-554:6 - Kenneth D. Doig, Jason Ellul, Andrew Fellowes, Ella R. Thompson, Georgina L. Ryland, Piers Blombery, Anthony T. Papenfuss, Stephen B. Fox:
Canary: an atomic pipeline for clinical amplicon assays. 555:1-555:7 - Valeria Montano, T. Jombart:
An Eigenvalue test for spatial principal component analysis. 562:1-562:7 - Jordi Martorell-Marugan, Daniel Toro-Domínguez, Marta E. Alarcón-Riquelme, Pedro Carmona-Saez:
MetaGenyo: a web tool for meta-analysis of genetic association studies. 563:1-563:6 - Nilesh Khiste, Lucian Ilie:
HISEA: HIerarchical SEed Aligner for PacBio data. 564:1-564:13 - Tianyu Kang, Wei Ding, Luoyan Zhang, Daniel Ziemek, Kourosh Zarringhalam:
A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data. 565:1-565:11 - Sumanta Ray, Sk Md Mosaddek Hossain, Lutfunnesa Khatun, Anirban Mukhopadhyay:
A comprehensive analysis on preservation patterns of gene co-expression networks during Alzheimer's disease progression. 579:1-579:21 - Fanchi Meng, Chen Wang, Lukasz A. Kurgan:
fDETECT webserver: fast predictor of propensity for protein production, purification, and crystallization. 580:1-580:11 - Gayathri Thillaiyampalam, Fabio Liberante, Liam Murray, Chris Cardwell, Ken I. Mills, Shu-Dong Zhang:
An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping. 581:1-581:16 - Yuhang Liu, Jinfeng Zhang, Xing Qiu:
Super-delta: a new differential gene expression analysis procedure with robust data normalization. 582:1-582:13 - Preeti Choudhary, Shailesh Kumar, Anand Kumar Bachhawat, Shashi Bhushan Pandit:
CSmetaPred: a consensus method for prediction of catalytic residues. 583:1-583:13 - Dennis E. te Beest, Steven W. Mes, Saskia M. Wilting, Ruud H. Brakenhoff, Mark A. van de Wiel:
Improved high-dimensional prediction with Random Forests by the use of co-data. 584:1-584:11 - Youngmahn Han, Dongsup Kim:
Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction. 585:1-585:9 - Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers, Matthew E. Hudson:
A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy. 586:1-586:12 - Chen Lyu, Bo Chen, Yafeng Ren, Donghong Ji:
Long short-term memory RNN for biomedical named entity recognition. 462 - Rex Shen, Lan Luo, Hui Jiang:
Identification of gene pairs through penalized regression subject to constraints. 466 - Chang Sik Kim, Martyn D. Winn, Vipin Sachdeva, Kirk E. Jordan:
K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity. 467 - Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda, Koji Tsuda:
RNA inverse folding using Monte Carlo tree search. 468 - Jebediah Rosen, Kyle Handy, André Gillan, Rob Smith:
JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals. 469 - Dawit Nigatu, Patrick Sobetzko, Malik Yousef, Werner Henkel:
Sequence-based information-theoretic features for gene essentiality prediction. 473 - Heidi E. L. Lischer, Kentaro K. Shimizu:
Reference-guided de novo assembly approach improves genome reconstruction for related species. 474 - Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann, Peter W. Hildebrand:
A fragment based method for modeling of protein segments into cryo-EM density maps. 475 - Paul M. Harrison:
fLPS: Fast discovery of compositional biases for the protein universe. 476 - Oriol Mazariegos-Canellas, Trien Do, Tim E. A. Peto, David W. Eyre, Anthony Underwood, Derrick W. Crook, David H. Wyllie:
BugMat and FindNeighbour: command line and server applications for investigating bacterial relatedness. 477 - Duc-Hau Le, Lieven P. C. Verbeke, Le Hoang Son, Dinh-Toi Chu, Van Huy Pham:
Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs. 479 - Oluwatosin Oluwadare, Jianlin Cheng:
ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data. 480 - Liying Yang, Yunyan Shen, Xiguo Yuan, Junying Zhang, Jianhua Wei:
Analysis of breast cancer subtypes by AP-ISA biclustering. 481 - Tao Zhu, Chengzhen Liang, Zhigang Meng, Sandui Guo, Rui Zhang:
GFF3sort: a novel tool to sort GFF3 files for tabix indexing. 482 - Maria Needhamsen, Ewoud Ewing, Harald Lund, David Gomez-Cabrero, Robert Adam Harris, Lara Kular, Maja Jagodic:
Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies. 486 - Richard Elias, David Hoksza:
TRAVeLer: a tool for template-based RNA secondary structure visualization. 487 - Rami Eitan, Ron Shamir:
Reconstructing cancer karyotypes from short read data: the half empty and half full glass. 488 - Eric C. Rouchka, Julia Chariker, David Tieri, Juw Won Park:
Correction to: Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2017: bioinformatics. 490 - Sérgio E. D. Dias, Ana Mafalda Martins, Quoc T. Nguyen, Abel João Padrão Gomes:
GPU-based detection of protein cavities using Gaussian surfaces. 493 - Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chang Feng, Guangqin Fan:
dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder. 494 - Yomtov Almozlino, Nir Atias, Dana Silverbush, Roded Sharan:
ANAT 2.0: reconstructing functional protein subnetworks. 495 - Khanh To Duc:
bcROCsurface: an R package for correcting verification bias in estimation of the ROC surface and its volume for continuous diagnostic tests. 503 - Nathan Sloat, Jui-Wen Liu, Susan J. Schroeder:
Swellix: a computational tool to explore RNA conformational space. 504 - Linlin Gao, Haiwei Pan, Qing Li, Xiaoqin Xie, Zhiqiang Zhang, Jinming Han, Xiao Zhai:
Brain medical image diagnosis based on corners with importance-values. 505 - Daniel Castillo, Juan Manuel Galvez, Luis Javier Herrera, Belén San Román, Fernando Rojas, Ignacio Rojas:
Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling. 506 - Rhys A. Farrer:
Synima: a Synteny imaging tool for annotated genome assemblies. 507 - Hongwei Ge, Liang Sun, Jinghong Yu:
Fast batch searching for protein homology based on compression and clustering. 508 - Kosai Al-Nakeeb, Thomas Nordahl Petersen, Thomas Sicheritz-Pontén:
Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data. 510 - Jie Tan, Matt Huyck, Dongbo Hu, René A. Zelaya, Deborah A. Hogan, Casey S. Greene:
ADAGE signature analysis: differential expression analysis with data-defined gene sets. 512 - Sudipta Acharya, Sriparna Saha, N. Nikhil:
Unsupervised gene selection using biological knowledge : application in sample clustering. 513 - Fen-Xiang Liu, Chunfa Tong, Shentong Tao, Jiyan Wu, Yuhua Chen, Dan Yao, Huogen Li, Jisen Shi:
MVQTLCIM: composite interval mapping of multivariate traits in a hybrid F1 population of outbred species. 515 - Marco Beccuti, Elisa Genuardi, Greta Romano, Luigia Monitillo, Daniela Barbero, Mario Boccadoro, Marco Ladetto, Raffaele A. Calogero, Simone Ferrero, Francesca Cordero:
HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. 516
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